Research workbench
Crystal structure of the alanine racemase from bacillus subtilis in the presence of only peg 4000 and magnesium chloride in the crystallization condition
Analyse Crystal structure of the alanine racemase from bacillus subtilis in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q72
- Type
- protein
- Length
- 1,544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase 2
- UniProt
- A0A386RMP5
- Ligands
- PLP, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Alanine racemase 2 | protein | 386 | 34% helix, 26% strand | A0A386RMP5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, D, E
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.77 | 0.89 | 49 | empty |
| 2 | 327 | 0.76 | 0.88 | 52 | empty |
| 3 | 295 | 0.75 | 0.88 | 54 | PLP, CL |
| 4 | 274 | 0.75 | 0.88 | 59 | PLP, CL |
| 5 | 294 | 0.75 | 0.87 | 63 | PLP, CL |
Interfaces
4 interfaces between chains.
- D–E · 3072 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3068 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 730 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 682 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor, 4 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 6Q72 · Crystal structure of the alanine racemase from Bacillus subtilis in the presence of only… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A386RMP5
- Elsewhere: RCSB PDB 6Q72 · PDBe 6Q72 · UniProt A0A386RMP5
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